Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera)

Antheraea assama, an economically important and scientifically unexplored Indian wild silkmoth, is unique among saturniid moths. For this species, a total of 87 microsatellite markers was derived from 35 000 expressed sequence tags and a microsatellite‐enriched sub‐genomic library. Forty individuals collected from Tura and West Garo Hills region of Northeast India were screened for each of these loci. Ten loci from expressed sequence tags and one from genomic library were found to be polymorphic. These microsatellite markers will be useful resources for population genetic studies of A. assama and other closely related species of saturniids. This is the first report on development of microsatellite markers for any saturniid species.     

Genetic Diversity and Population Structure of Alnus hirsuta (Betulaceae) in Korea

Alnus hirsuta in Korea was measured to estimate the amount and pattern of genetic diversity and population structure. The mean genetic diversity within populations was 0.166. Korean alder populations have slightly high levels of genetic diversity compared to those of two Canadian alder species. The genetic differentiation among populations accounted for 9% of the total variation. The rate of gene flow was estimated high (Nm=2.63). Analysis of inbreeding coefficient, calculated for all polymorphic loci in each population, showed a substantial heterozygote deficiency relative to Hardy-Weinberg expectations. The mean G _ST value of A. hirsuta in Korea was 0.087. The low value of G _ST in this species, reflecting little spatial genetic differentiation, may indicate extensive gene flow. A relationship between the mean heterozygosity and annual rainfall showed a positive relationship (r ²=0.54, F=4.67). Received 8 August 1998/ Accepted in revised form 7 July 1999     

Genetic Diversity and Population Structure of Teucrium polium (Lamiaceae) in Tunisia

Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon’s index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G _ST and Φ_ST statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li’s coefficient showed that individuals from each population clustered together. In a dendrogram using the Φ_ST distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels.     

Genetic Diversity and Population Structure of Juniperus rigida (Cupressaceae) and Juniperus coreana

Enzyme electrophoresis was used to estimate genetic diversity and population structure of Juniperus rigida (Cupressaceae) and Juniperus coreana in Korea. In J. rigida, 16 of the 22 loci (72.7%) showed detectable polymorphism. Genetic diversity (0.224) was higher than average values for species with similar life history traits. The endemic species (J. coreana) was found to have fewer alleles per locus (1.39 vs. 1.61), fewer alleles per polymorphic locus (2.42 vs. 2.63), lower percent polymorphic locus (54.6 vs. 72.7%), and lower diversity (0.199 vs. 0.224) than J. rigida. These genetic diversity parameters indicated that J. coreana was genetically depauperate relative to its presumptive progenitor, J. rigida. Analysis of fixation indices showed a substantial deficiency of heterozygotes relative to Hardy–Weinberg expectations suggesting inbreeding in J. coreana. The G _ST values of J. rigida and J. coreana were 0.173 and 0.118 respectively. The indirect estimate of gene flow based on mean G _ST was moderate (Nm = 1.19 for J. rigida and 1.86 for J. coreana). This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

Plant Molecular Biology Reporter - Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant...     

Genetic Diversity and Population Structure of Acacia senegal (L) Willd. in Kenya

The level of genetic diversity and population structure of Acacia senegal variety kerensis in Kenya was examined using seven polymorphic nuclear microsatellite loci and two chloroplast microsatellite loci. In both chloroplast and nuclear datasets, high levels of genetic diversity were found within all populations and genetic differentiation among populations was low, indicating extensive gene flow. Analysis of population structure provided support for the presence of two groups of populations, although all individuals had mixed ancestry. Groups reflected the influence of geography on gene flow, with one representing Rift Valley populations whilst the other represented populations from Eastern Kenya. The similarities between estimates derived from nuclear and chloroplast data suggest highly effective gene dispersal by both pollen and seed in this species, although population structure appears to have been influenced by distributional changes in the past. The few contrasts between the spatial patterns for nuclear and chloroplast data provided additional support for the idea that, having fragmented in the past, groups are now thoroughly mixed as a result of extensive gene flow. For the purposes of conservation and in situ management of genetic resources, sampling could target a few, large populations ideally distributed among the spatial groups identified. This should ensure the majority of extant variation is preserved, and facilitate the investigation of variation in important phenotypic traits and development of breeding populations.     

Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop''s genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.     

Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ?K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.     

Genetic Diversity and Population Structure of Theileria annulata in Oman

Background

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.

Methods

Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.

Results

We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise F_ST values being less than 0.03. Slightly higher F_ST values (G_ST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia.

Conclusion

Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman.     

Genetic Diversity and Population Structure of the Brachiaria brizantha Germplasm

Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed.     

Temporal Variation in Genetic Diversity and Structure of a Lotic Population of Burkholderia (Pseudomonas) cepacia

The genetic structure and temporal patterns of genetic diversity in a population of Burkholderia (Pseudomonas) cepacia, isolated from a southeastern blackwater stream, were investigated by multilocus enzyme electrophoresis. Allelic variation in seven structural gene loci was monitored at a single stream location at 0, 6, 12, and 24 h and at 2, 4, 8, 16, and 32 days. Over the length of the study, 217 isolates were collected, from which 65 unique electrophoretic types (ETs) were identified. Most of these ETs were present at only one or two time periods and were considered transients; however, one resident ET was particularly abundant (64 of the 217 isolates [29.4%]) and was found at all time points except day 32. The mean genetic diversity of the entire population was 0.520, and the index of association (a measure of multilocus linkage disequilibrium) was 1.33. These results, taken in conjunction with a previous study focusing on spatial patterns of genetic diversity in lotic B. cepacia, show that these bacterial populations exhibit greater variability among sites than within a site over time, suggesting relative stability over short time periods.     

Genetic Variation within Native Populations of Endemic Silkmoth Antheraea assamensis (Helfer) from Northeast India Indicates Need for In Situ Conservation

A. assamensis is a phytophagous Lepidoptera from Northeast India reared on host trees of Lauraceae family for its characteristic cocoon silk. Source of these cocoons are domesticated farm stocks that crash frequently and/or wild insect populations that provide new cultures. The need to reduce dependence on wild populations for cocoons necessitates assessment of genetic diversity in cultivated and wild populations. Molecular markers based on PCR of Inter-simple sequence repeats (ISSR) and simple sequence repeats (SSR) were used with four populations of wild insects and eleven populations of cultivated insects. Wild populations had high genetic diversity estimates (H_i = 0.25; H_S = 0.28; H_E = 0.42) and at least one population contained private alleles. Both marker systems indicated that genetic variability within populations examined was significantly high. Among cultivated populations, insects of the Upper Assam region (H_i = 0.19; H_S = 0.18; H_E = 0) were genetically distinct (F_ST = 0.38 with both marker systems) from insects of Lower Assam (H_i = 0.24; H_S = 0.25; H_E = 0.3). Sequencing of polymorphic amplicons suggested transposition as a mechanism for maintaining genomic diversity. Implications for conservation of native populations in the wild and preserving in-farm diversity are discussed.     

Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure

The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.     

Population Structure and Genetic Diversity of Common Bean Accessions from Brazil

Plant Molecular Biology Reporter - Brazil can be considered a secondary center of common bean diversification (Phaseolus vulgaris L.), and the landraces grown throughout Brazil are valuable sources...     

Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China

Miscanthus is a perennial rhizomatous C4 grass native to East Asia. Endowed with great biomass yield, high ligno-cellulose composition, efficient use of radiation, nutrient and water, as well as tolerance to stress, Miscanthus has great potential as an excellent bioenergy crop. Despite of the high potential for biomass production of the allotriploid hybrid M. ×giganteus, derived from M. sacchariflorus and M. sinensis, other options need to be explored to improve the narrow genetic base of M. ×giganteus, and also to exploit other Miscanthus species, including M. sinensis (2n = 2x = 38), as bioenergy crops. In the present study, a large number of 459 M. sinensis accessions, collected from the wide geographical distribution regions in China, were genotyped using 23 SSR markers transferable from Brachypodium distachyon. Genetic diversity and population structure were assessed. High genetic diversity and differentiation of the germplasm were observed, with 115 alleles in total, a polymorphic rate of 0.77, Nei’s genetic diversity index (He) of 0.32 and polymorphism information content (PIC) of 0.26. Clustering of germplasm accessions was primarily in agreement with the natural geographic distribution. AMOVA and genetic distance analyses confirmed the genetic differentiation in the M. sinensis germplasm and it was grouped into five clusters or subpopulations. Significant genetic variation among subpopulations indicated obvious genetic differentiation in the collections, but within-subpopulation variation (83%) was substantially greater than the between-subpopulation variation (17%). Considerable phenotypic variation was observed for multiple traits among 300 M. sinensis accessions. Nine SSR markers were found to be associated with heading date and biomass yield. The diverse Chinese M. sinensis germplasm and newly identified SSR markers were proved to be valuable for breeding Miscanthus varieties with desired bioenergy traits.     

Genetic Diversity and Population Structure in Chinese Indigenous Poplar (Populus simonii) Populations Using Microsatellite Markers

Populus simonii Carr. is an important ecological and commercial breeding species in northern China; however, human interference during the last few centuries has led to the reduction and fragmentation of natural populations. To evaluate genetic diversity and differentiation within and among existing populations, we used 20 microsatellite markers to examine the genetic variation and structure of 16 natural populations. Our results indicated that the level of genetic diversity differed among populations, with average number of alleles per locus (AR) and expected heterozygosity (H _e) ranging from 3.7 to 6.11 and 0.589 to 0.731, respectively. A marginal population from Qilian in the Qinghai–Tibetan Plateau showed the highest values (AR?=?6.11, H _e?=?0.731), and the Zhangjiakou and Yishui populations showed the lowest values (AR?=?4.08, H _e?=?0.589 and AR?=?3.7, H _e?=?0.604). The inbreeding coefficient (F _IS) values for all populations were positive, which indicated an excess of homozygotes. The microsatellites allowed the identification of a significant subpopulation structure (K?=?3), consistent with an isolation by distance model for P. simonii populations. Additionally, molecular variance analysis revealed that 14.2 % of the variation resided among populations, and 85.8 % could be attributed to variation within populations. These data provide valuable information for natural resource conservation and for optimization of breeding programs in the immediate future.     

中国木棉居群的遗传多样性

采用ISSR分子标记技术研究了干热河谷地区（云南的元江、元谋、巧家、保山4个居群）、干热地区（广西、海南2个居群）和湿热地区（西双版纳1个居群）木棉（Bombax malabaricum）居群的遗传多样性。用筛选出的10条引物,对110个个体进行了扩增,共检测到142个位点,多态位点百分率PPB=90.14%,Nei′s基因多样性指数H=0.2530,Shannon′s信息指数I为0.3864;居群间的遗传分化系数GST=0.1870,用AMOVA分析得出的Фst=0.177;研究结果表明木棉具有较高水平的遗传多样性,而居群间的遗传分化较低。我们推断木棉丰富的遗传多样性和有效的基因流是其较好适应性的重要因素。此外,我们建议在干热河谷地区对木棉进行引种时,要在居群内大量取样,并尽可能对不同居群进行取样。     

白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对白鱼(Anabarilius grahami)DNA进行PCR扩增,获得了白鱼线粒体DNA控制区基因全序列(930bp)。控制区T、C、A和G碱基组成为29.8%、22.5%、33.0%和14.7%。对照其他已报道的鱼类控制区结构,对白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列(CSB-F、CSB-D、CSB-1、CSB-2、CSB-3)。同时运用DNA分析软件对白鱼一个驯养种群(中国科学院昆明动物研究所珍稀鱼类繁育中心)及两个自然地理种群(江川县明星鱼洞、江川县牛摩村)进行了遗传多样性分析。结果显示:两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好。